no AC tag in output vcf #107
Description
Hello,
I'm running longshot for some ONT cDNA data using the following command:
longshot --bam barcode22_flair_aligned.bam --ref ${GENOME_FASTA} --out barcode22_flair_aligned_longshot.vcf --out_bam barcode22_flair_aligned_longshot.bam
It ran successfully, however, I'm missing an AC tag which is needed for downstream. See below output of the vcf file:
##INFO=<ID=SC,Number=1,Type=String,Description="Reference Sequence in 21-bp window around variant.">
##FILTER=<ID=dn,Description="In a dense cluster of variants">
##FILTER=<ID=dp,Description="Exceeds maximum depth">
##FILTER=<ID=sb,Description="Allelic strand bias">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase Set">
##FORMAT=<ID=UG,Number=1,Type=String,Description="Unphased Genotype (pre-haplotype-assembly)">
##FORMAT=<ID=UQ,Number=1,Type=Float,Description="Unphased Genotype Quality (pre-haplotype-assembly)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
chr1 632106 . T C 21 PASS DP=7;AM=2;MC=0;MF=0.000;MB=0.000;AQ=8.49;GM=1;DA=44;MQ10=0.32;MQ20=0.16;MQ30=0.02;MQ40=0.00;MQ50=0.00;PH=20.53,9.48,46.37,0.56;SC=CCCTAGGATTTATTTTTCTT
T; GT:GQ:DP:AD:PS:UG:UQ 1/1:10:7:0,3:.:1/1:6.43
chr1 632109 . T C 9 PASS DP=7;AM=2;MC=0;MF=0.000;MB=0.000;AQ=10.38;GM=1;DA=46;MQ10=0.30;MQ20=0.15;MQ30=0.02;MQ40=0.00;MQ50=0.00;PH=8.64,0.68,42.73,20.70;SC=TAGGATTTATTTTTCTTTT
CA; GT:GQ:DP:AD:PS:UG:UQ 0|1:9:7:1,2:632109:0/1:6.01
chr1 632160 . A G 311 PASS DP=16;AM=1;MC=0;MF=0.000;MB=0.000;AQ=13.40;GM=1;DA=80;MQ10=0.39;MQ20=0.20;MQ30=0.09;MQ40=0.00;MQ50=0.00;PH=310.86,171.00,55.84,0.00;SC=CAAACTCATCACTAG
ACATCG; GT:GQ:DP:AD:PS:UG:UQ 1/1:56:16:0,15:.:1/1:41.03
chr1 632199 . C T 378 PASS DP=17;AM=0;MC=0;MF=0.000;MB=0.000;AQ=24.43;GM=1;DA=86;MQ10=0.40;MQ20=0.20;MQ30=0.08;MQ40=0.00;MQ50=0.00;PH=377.35,176.87,76.84,0.00;SC=ACGTTGTAGCCCACT
TCCACT; GT:GQ:DP:AD:PS:UG:UQ 1/1:77:17:0,17:.:1/1:47.90
chr1 632226 . A G 353 PASS DP=18;AM=0;MC=0;MF=0.000;MB=0.000;AQ=24.42;GM=1;DA=87;MQ10=0.40;MQ20=0.21;MQ30=0.08;MQ40=0.00;MQ50=0.00;PH=352.73,195.21,31.06,0.00;SC=TATCAATAGGAGCTG
TATTTG; GT:GQ:DP:AD:PS:UG:UQ 1/1:32:18:1,17:.:1/1:26.50
chr1 632403 . T C 155 PASS DP=21;AM=7;MC=0;MF=0.000;MB=0.000;AQ=8.83;GM=1;DA=109;MQ10=0.39;MQ20=0.19;MQ30=0.07;MQ40=0.01;MQ50=0.00;PH=154.91,42.06,0.01,26.60;SC=ACTCGGACTATCCCGA
TGCAT; GT:GQ:DP:AD:PS:UG:UQ 1|0:27:21:4,10:632109:0/1:23.67
Am I missing a parameter or is there a way to add the AC tag back into the file please?
Thank you,
Szi